When you do the restart/reboot of your computer, is mIRC an active application, or have you shut it down previously?
If it is an active application, then the fault may lie in the fact that the information in the ini files may be being re-written due to the closure of mIRC when the system actually does reboot.
Sometimes it's a clean shutdown, other times it's not. However, I can load it up and it'll still be remembered, then later the customizations are gone.
One option that may help is to use the /flushini command on a semi-regular (or regular) basis. Also, if you remember to close mIRC before restarting/rebooting your system, this should also prevent what you are experiencing.
I would think that once I've added the entries and closed/reopened mIRC and the entries are still there, that they would be there from that point on. But what's happening is that any customizations are literally being tossed away despite that.